Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01016900.1 Corchorus olitorius cultivar O-4 contig16933, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 11511
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35


Found at i:3141 original size:12 final size:13

Alignment explanation


    Indices: 3124--3158  Score: 63
    Period size: 12  Copynumber: 2.8  Consensus size: 13

       3114 CATCGATACC

                         
       3124 TCGATATATCCG-
          1 TCGATATATCCGT

                         
       3136 TCGATATATCCGT
          1 TCGATATATCCGT

                      
       3149 TCGATATATC
          1 TCGATATATC

       3159 AATAAATATC


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  12   12  0.55
  13   10  0.45

ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37


Consensus pattern (13 bp):   
TCGATATATCCGT

Found at i:5960 original size:19 final size:19

Alignment explanation


    Indices: 5936--5973  Score: 76
    Period size: 19  Copynumber: 2.0  Consensus size: 19

       5926 ACCCATATCG

                               
       5936 GCTTTGATGGTTATGCCTC
          1 GCTTTGATGGTTATGCCTC

                               
       5955 GCTTTGATGGTTATGCCTC
          1 GCTTTGATGGTTATGCCTC

       5974 TGTGCAATCA


Statistics
Matches: 19,  Mismatches: 0, Indels: 0
        1.00            0.00        0.00

Matches are distributed among these distances:
  19   19  1.00

ACGTcount: A:0.11, C:0.21, G:0.26, T:0.42


Consensus pattern (19 bp):   
GCTTTGATGGTTATGCCTC

Found at i:7700 original size:107 final size:107

Alignment explanation


    Indices: 7562--7754  Score: 323
    Period size: 107  Copynumber: 1.8  Consensus size: 107

       7552 AGGTTTTATA

                                    *                 *     * *              
       7562 TTATAGAGTTTTAAAAATAAAATATAAAACTAATTTCACTAATTTTAGTCTCAAATTAAAATTTT
          1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT

                       *                              
       7627 ATTTTTATTTTTAGGGTAAATTTCAAAATTAACAATTTGTTG
         66 ATTTTTATTTTAAGGGTAAATTTCAAAATTAACAATTTGTTG

                         *            *                                      
       7669 TTATAGAGTTTTAGAAATAAAATACAGAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
          1 TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT

                                 
       7734 ATTTTTATTTTAAGGGTAAAT
         66 ATTTTTATTTTAAGGGTAAAT

       7755 AATTTGTTAC


Statistics
Matches: 79,  Mismatches: 7, Indels: 0
        0.92            0.08        0.00

Matches are distributed among these distances:
 107   79  1.00

ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42


Consensus pattern (107 bp):   
TTATAGAGTTTTAAAAATAAAATACAAAACTAATTTCACTAAGTTTAGCCCCAAATTAAAATTTT
ATTTTTATTTTAAGGGTAAATTTCAAAATTAACAATTTGTTG

Found at i:10986 original size:31 final size:29

Alignment explanation


    Indices: 10921--10987  Score: 80
    Period size: 31  Copynumber: 2.2  Consensus size: 29

      10911 ATGCAATTTG

                              *   *      
      10921 GGATATAACGTTACAAAATAAGTAATTAA
          1 GGATATAACGTTACAAAACAAGCAATTAA

            *                    *         
      10950 AGATATAACGTTACGAAAAGCGAGCAATTAA
          1 GGATATAACGTTAC-AAAA-CAAGCAATTAA

                   
      10981 GGATATA
          1 GGATATA

      10988 GTCCGTTAAG


Statistics
Matches: 31,  Mismatches: 5, Indels: 2
        0.82            0.13        0.05

Matches are distributed among these distances:
  29   13  0.42
  30    4  0.13
  31   14  0.45

ACGTcount: A:0.49, C:0.09, G:0.18, T:0.24


Consensus pattern (29 bp):   
GGATATAACGTTACAAAACAAGCAATTAA

Found at i:11143 original size:31 final size:31

Alignment explanation


    Indices: 11108--11186  Score: 131
    Period size: 31  Copynumber: 2.5  Consensus size: 31

      11098 CTAACTGATT

                                 **        
      11108 ATATCCTTAATTGCTTGAAATCGAAAACGTC
          1 ATATCCTTAATTGCTTGAAATAAAAAACGTC

                                          *
      11139 ATATCCTTAATTGCTTGAAATAAAAAACGTT
          1 ATATCCTTAATTGCTTGAAATAAAAAACGTC

                             
      11170 ATATCCTTAATTGCTTG
          1 ATATCCTTAATTGCTTG

      11187 TTTTGTAACG


Statistics
Matches: 45,  Mismatches: 3, Indels: 0
        0.94            0.06        0.00

Matches are distributed among these distances:
  31   45  1.00

ACGTcount: A:0.35, C:0.16, G:0.11, T:0.37


Consensus pattern (31 bp):   
ATATCCTTAATTGCTTGAAATAAAAAACGTC

Found at i:11236 original size:61 final size:60

Alignment explanation


    Indices: 11133--11247  Score: 158
    Period size: 61  Copynumber: 1.9  Consensus size: 60

      11123 TGAAATCGAA

                                      *        *        *               
      11133 AACGTCATATCCTTAATTGCTTGAAATAAAAAACGTTATATCCTTAATTGCTTGTTTTGT
          1 AACGTCATATCCTTAATTGCTTGAAACAAAAAACGCTATATCCTAAATTGCTTGTTTTGT

                 *                  ***                            
      11193 AACGTTATATCCTTAAATTGCTTGCGGCAAAAAACGCTATATCCTAAATTGCTTG
          1 AACGTCATATCCTT-AATTGCTTGAAACAAAAAACGCTATATCCTAAATTGCTTG

      11248 CTTATCATCT


Statistics
Matches: 47,  Mismatches: 7, Indels: 1
        0.85            0.13        0.02

Matches are distributed among these distances:
  60   13  0.28
  61   34  0.72

ACGTcount: A:0.32, C:0.17, G:0.13, T:0.37


Consensus pattern (60 bp):   
AACGTCATATCCTTAATTGCTTGAAACAAAAAACGCTATATCCTAAATTGCTTGTTTTGT
Done.